fusion-tools 0.0.5

Utility functions for generating, saving, and converting annotation files

fusion-tools

Some utilities, accession, and visualization tools for data derived from FUSION (Functional Unit State Identification in WSIs).

Installation

$ pip install fusion-tools

Usage

fusion-tools is intended to bring some of the functionality found in FUSION to developers working with whole slide images (WSIs) stored locally.

One such example would be the LocalTileServer and SlideMap class:

from fusion_tools import Visualization
from fusion_tools.tileserver import LocalTileServer
from fusion_tools.components import SlideMap

import threading

path_to_slide = '/path/to/wsi.svs'

tile_server_port = '8050'
tile_server = LocalTileServer(
    local_image_path = path_to_slide
)

new_thread = threading.Thread(target = tile_server.start, name = 'tile-server', args = [tile_server_port])
new_thread.daemon = True
new_thread.start()

vis_session = Visualization(
    components = [
        [
            SlideMap(
                tile_server = tile_server,
                annotations = None
            )
        ]
    ]
)

vis_session.start()

The Visualization class lets users construct custom layouts of different tools by passing a list containing rows, columns, and tabs. (e.g. [ [column in row 1], [ [ tab 1 in column 2 in row 1, tab 2 in column 2 in row 1] ], [ [ column 1 in row 2 ] ] ] )

import threading
from fusion_tools import Visualization
from fusion_tools.tileserver import LocalTileServer
from fusion_tools.components import SlideMap, OverlayOptions, PropertyViewer
from fusion_tools.utils.shapes import load_aperio


path_to_slide = '/path/to/wsi.svs'
path_to_annotations = '/path/to/aperio_annotations.xml'

annotations = load_aperio(path_to_annotations)

tile_server_port = '8050'
tile_server = LocalTileServer(
    local_image_path = path_to_slide
)

# Starting LocalTileServer
new_thread = threading.Thread(target = tile_server.start, name = 'local_tile_server', args = [tile_server_port])
new_thread.daemon = True
new_thread.start()

vis_session = Visualization(
    components = [
        [
            SlideMap(
                tile_server = tile_server,
                annotations = annotations
            ),
            [
                OverlayOptions(
                    geojson_anns = annotations
                ),
                PropertyViewer(
                    geojson_list = annotations
                )
            ]
        ]
    ]
)

vis_session.start()

Contributing

please

License

fusion-tools was created by Samuel Border. It is licensed under the terms of the Apache 2.0 License